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Groundbreaking Paper Shows Thousands of New Genes Needed for the Origin of Animals

Someday we may get tired of being vindicated. But not yet! Günter Bechly recently discussed a new paper that confirmed Stephen Meyer’s claims in Darwin’s Doubt that arthropods appeared abruptly in the Cambrian explosion, without evolutionary precursors in the Precambrian. Another recent groundbreaking paper in Nature Communications has also provided massive confirmation of Meyer’s arguments in the book that new genes were required at the origin of animals.

An Uncontroversial Idea?

Whether you’re an evolutionary biologist or a proponent of intelligent design, the notion that the origin of animals required new genes — even numerous new genes — might strike you as uncontroversial. But this claim was strongly challenged by UC Berkeley evolutionary paleontologist Charles Marshall who reviewed Darwin’s Doubt in the journal Science. It actually became a centerpiece of the debate between Marshall and Meyer about the Cambrian explosion. (For replies to Marshall, see here, here, here, here, here, and here.) Here’s the substance of Marshall’s counter-argument, as it was published in Science:

His [Meyer’s] case against current scientific explanations of the relatively rapid appearance of the animal phyla rests on the claim that the origin of new animal body plans requires vast amounts of novel genetic information coupled with the unsubstantiated assertion that this new genetic information must include many new protein folds. In fact, our present understanding of morphogenesis indicates that new phyla were not made by new genes but largely emerged through the rewiring of the gene regulatory networks (GRNs) of already existing genes (1).

Marshall didn’t stop there. He went further, saying that Meyer has an “idiosyncratic fixation with new protein folds” and “an outdated understanding of morphogenesis” — all due to Meyer’s supposedly inaccurate claims that the Cambrian explosion would have required the origin of many new genes. Now this new paper, “Reconstruction of the ancestral metazoan genome reveals an increase in genomic novelty,” provides a direct refutation of Marshall’s insistence that the origin of animals didn’t require lots of new genes.

From the paper:

Recent studies show that many genes typically associated with metazoan functions actually pre-date animals themselves, supporting functional co-option of ‘unicellular genes’ during the genesis of metazoans.

However, the role of genome novelty in animal origins has not been fully evaluated. We hypothesize that genomic novelty had a major impact in this transition, particularly involving biological functions which are hallmarks of animal multicellularity (gene regulation, signalling, cell adhesion, and cell cycle). Here we apply a comparative genomics approach using sophisticated methods, newly developed programs, and a comprehensive taxon sampling. The reconstruction of the ancestral genome of the last common ancestor of animals shows a set of biological functions similar to other eukaryote ancestors, while revealing an unexpected expansion of gene diversity. These analyses also highlight 25 groups of genes only found in animals that are highly retained in all their genomes, with essential functions linked to animal multicellularity.

They conclude that “many new” genes were necessary during the origin of animals:

Thus, the first animal genome was not only showing a higher proportion of Novel HG [homology groups], but these also perform major multicellular functions in the modern fruit fly genome. The implication is that the transition was accompanied by an increase of genomic innovation, including many new, divergent, and subsequently ubiquitous genes encoding regulatory functions associated with animal multicellularity.

These “homology groups” (HGs) are exactly what they sound like — groups of genes that are similar. A “novel HG” is a group of genes that is found in animals, or particular groups of animals, that do not exist elsewhere. This indicates that these groups of genes were necessary for these animals to exist.

An Open-Access Paper; Check It Out

Just how many novel HGs (and genes) are we talking about? The paper is open access, and readers can easily see that Figure 1 shows that while 1189 HGs are necessary for the origin of Metazoa (multicellular organisms with differentiated tissues), as one moves farther up the animal tree, hundreds if not thousands of additional novel HGs are required:

For the origin of Bilateria (animals with two-sided symmetry — a left and a right side), an additional 1580 HGs are required! According to Figure 2, about 16 percent of the bilaterian genome entails novel HGs!

We discovered the first animal had an exceptional number of novel genes, four times more than other ancestors. This means the evolution of animals was driven by a burst of new genes not seen in the evolution of their unicellular ancestors.

Straightforward Methodology

The methodology used by the paper is relatively straightforward. It compared the genomes of modern-day animals to determine what genes they share in common. This was then used to determine which genes were present in the genomes of the putative common ancestors of various animal groups. By comparing the common genes shared at different levels of the animal taxonomic hierarchy, they were able to determine how many new genes would have to appear at various stages of animal evolution.

During the debate, Marshall amplified this argument by claiming that Meyer’s argument presupposed an outdated “1980s model of the way genes operate” and that his book “confronted a different set of problems that hark back to an older age.” According to Marshall, biologists no longer believe that building the diverse forms of Cambrian animals would require evolving new genes (or, at least, many new genes). Instead, Marshall argued, again, that new body plans could be generated by rewiring networks of already-existing genes, especially those which are part of the developmental gene regulatory networks (dGRNs) that control the timing and expression of pre-existing genes during animal development. Marshall pointed out that animals have far fewer genes than we once expected, and that today it is thought that “animals use essentially the same genes, just deployed slightly differently.” By changing the deployment of those genes — by rewiring their dGRNs — Marshall thinks new body plans can arise.

It’s worth noting that throughout the debate, Meyer didn’t concede on Marshall’s claims that new genes aren’t necessary. Instead, he argued that even if we assume for the sake of the argument that Marshall is right that new genes aren’t necessary to build animals, that doesn’t solve the problem because rewiring the dGRNs still requires a huge input of information.

Dual Information Problems

In that regard, the new Nature Communications paper shows that Marshall’s evolutionary viewpoint faces information problems on two fronts. Figure 2c indicates that by far the largest classes of novel genes in the metazoa are related to generating nucleic acid binding proteins, and transcription factors. This suggests that not only were many new genes needed in the origin of Metazoa, but those new genes had profound influences on gene regulation — i.e., they were involved with rewiring of GRNs.

Thus both Meyer and Marshall were right that dGRNs needed to be wired to build animals — but they were right in the most devastating manner for Darwinism, namely that the rewiring of the dGRNS was mediated by entirely new genes. The paper’s demonstration that thousands of new genes would have been required during the origin of animals is nothing short of a spectacular vindication of Meyer’s perspective on this question, and a strong falsification of Marshall’s viewpoint.